Domains Homeodomains

Figure 9.12 Schematic diagram of the structure of the heterodimeric yeast transcription factor Mat a2-Mat al bound to DNA. Both Mat o2 and Mat al are homeodomains containing the helix-turn-helix motif. The first helix in this motif is colored blue and the second, the recognition helix, is red. (a) The assumed structure of the Mat al homeodomain in the absence of DNA, based on Its sequence similarity to other homeodomains of known structure, (b) The structure of the Mat o2 homeodomain. The C-terminal tail (dotted) is flexible in the monomer and has no defined structure, (c) The structure of the Mat a 1-Mat a2-DNA complex. The C-terminal domain of Mat a2 (yellow) folds into an a helix (4) in the complex and interacts with the first two helices of Mat a2, to form a heterodimer that binds to DNA. (Adapted from B.J. Andrews and M.S. Donoviel, Science 270 251-253, 1995.)...

Figure 9.13 The DNA-binding region of the protein Oct-1, the POU region (green), comprises two domains, the POU-specific domain (dark green) and the POU homeodomain (light green) joined by a linker region (blue). These two domains bind to DNA in a tandem arrangement.

Figure 9.14 The two domains of the POU region bind in tandem on opposite sides of the DNA double helix. Both the POU-specific domain and the POU homeodomain have a helix-turn-helix motif (blue and red) which binds to DNA with their recognition helices (red) in the major groove. The linker region that joins these domains is partly disordered. (Adapted from J.D. Klemm et al.. Cell 77 21-32, 1994.)...

Both domains of the POU region bind to DNA by the usual combination of non specific binding to the DNA backbone and specific binding to the bases. The contacts between the homeodomain and DNA are similar to those of the engrailed homeodomain (compare Figures 9.10b and 9.15a) and the... 

POU regions bind to DNA by two tandemly oriented helix-turn-helix motifs Much remains to be learnt about the function of homeodomains in vivo Understanding tumorigenic mutations The monomeric p53 polypeptide chain is divided in three domains The oligomerization domain forms tetramers The DNA-binding domain of p53 is an antiparallel P barrel... 

The paired box is another sequence motif that is very well conserved during evolution and is found in a number of genes known to be of developmental significance in lower organisms. The paired box encodes the 128-amino acid paired domain, which binds DNA(Chalapakis et al., 1991), and shows similarity, with a helix-tum-helix motif, to the homeodomain. 

Schrick, K., Nguyen, D., Karlowski, W. M., and Mayer, K. F. 2004. START lipid/sterol-binding domains are amplified in plants and are predominantly associated with homeodomain transcription factors. Genome Biol., 5(6) R41. 

The specific domains that recognize KMe have been described within several protein families the so-called "royal family" of Tudor, Agenet, chromo, PWWP, and MBT domains the plant homeodomain (PHD) the WD40 repeat protein—WDR5 and ankyrin repeats [37,38]. Given the rapid rate of progress in this area, the relatively low affinity of these interactions (Kd values typically 10-100 jjM), the wide variety of... 

Answen Q Proteins with SH2 domains might bind to the insulin receptor substrate-1 (IRS-1) to transmit signals from the insulin receptor, a tyrosine kinase type of receptor. PI-3 kinase is an example of an SH2 domain protein. SH2 domains are not involved in DNA binding (choices A and D). Examples of protein domains that bind DNA include zinc fingers (steroid receptors), leudne zippers (CREB protein), and helix-turn-helbc proteins (homeodomain proteins),... 

Several DNA-binding motifs have been described, but here we focus on two that play prominent roles in the binding of DNA by regulatory proteins the helix-tum-helix and the zinc finger. We also consider a type of DNA-binding domain—the homeodomain—found in some eukaryotic proteins. 

Homeodomain Another type of DNA-binding domain has been identified in a number of proteins that function as transcriptional regulators, especially during eukaryotic... 

Regulatory proteins are DNA-binding proteins that recognize specific DNA sequences most have distinct DNA-binding domains. Within these domains, common structural motifs that bind DNA are the helix-turn-helix, zinc finger, and homeodomain. 

These domains are often found as repeats in proteins that are involved in diverse biochemical processes. The LIM domains are thought to fimction as protein interaction modules, mediating specific contacts between members of functional complexes and modnlating the activity of some of the constituent proteins. Gronp 1 of the LIM proteins contain the LIM homeodomain (LHX), LIMK (LIM kinases) and LMO (rhombotin) subfamilies. 

Homeodomain A domain in a protein that is encoded for by a homeobox these proteins are transcription factors. Homeodomains are approximately 60 amino acids... 

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